Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(biomaRt)
library(fgsea)
library(goseq)

theme_set(theme_classic())
graph_weight = params$graph_weight
graph_weight
## [1] "5.0"

Check enrichment of gene sets

Read in gene info and gene set assignments

cell_type_name = "CD8T"
file_tag = sprintf("%s_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##   24.00   25.00   25.00   25.52   26.00   27.00
length(n_genes)
## [1] 40
sort(n_genes)
##  [1] 24 24 24 24 24 24 24 25 25 25 25 25 25 25 25 25 25 25 25 25 25 26 26 26 26
## [26] 26 26 26 26 26 26 27 27 27 27 27 27 27 27 27
sum(n_genes)
## [1] 1021

Find gene symbols

Find gene symbols from bioMart.

All the gene symbols that can be found in bioMart are consistent with what we have. So no need to run it.

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"), 
                filters = "external_gene_name", 
                values = assayed_genes, 
                mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]

table(assayed_genes %in% gene_BM$external_gene_name)

t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]

table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}
## [1] "C7orf55"
## [1] "FMC1-LUC7L2" "FMC1"       
## [1] "MARS"
## [1] "MARS1" "SLA2" 
## [1] "QARS"
## [1] "EPRS1" "QARS1"
## [1] "APITD1"
## [1] "CENPS-CORT" "CENPS"     
## [1] "HIST1H2BC"
## [1] "H2BC5" "H2BC4"
table(is.na(a2s))
## 
## FALSE  TRUE 
##  1120   139
table(a2s == assayed_genes, useNA = 'ifany')
## 
## FALSE  TRUE  <NA> 
##    71  1049   139
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]
##      sym_in_data   sym_limma
##  1:        ZNRD1      POLR1H
##  2:      C2orf43        LDAH
##  3:       FAM45A     DENND10
##  4:        MTERF      MTERF1
##  5:        NARG2        ICE2
##  6:     C6orf203      MTRES1
##  7:       HRSP12        RIDA
##  8:        FOPNL       CEP20
##  9:         WARS       WARS1
## 10:         LINS       LINS1
## 11:       RRNAD1    METTL25B
## 12:      FAM122B      PABIR2
## 13:       WDYHV1       NTAQ1
## 14:    HIST1H2BD       H2BC5
## 15:       AGPAT6       GPAT4
## 16:     C1orf123        CZIB
## 17:     KIAA1841       SANBR
## 18:      C2orf44        WDCP
## 19:      TMEM155      SMIM43
## 20:      C7orf55 FMC1-LUC7L2
## 21:      C9orf89      CARD19
## 22:     C11orf82       DDIAS
## 23:     XRCC6BP1       ATP23
## 24:         MARS       MARS1
## 25:     C19orf55     PROSER3
## 26:    HIST1H2AE       H2AC8
## 27:         QARS       EPRS1
## 28:       APITD1  CENPS-CORT
## 29:      CCDC101       SGF29
## 30:        PDDC1       GATD1
## 31:      EFCAB4A     CRACR2B
## 32:      EIF2S3L     EIF2S3B
## 33:    HIST1H2BC       H2BC5
## 34:          WRB        GET1
## 35:     TMEM194B       NEMP2
## 36:     HIST1H4C        H4C3
## 37:     HIST1H4J       H4C11
## 38:       ZNF720      KRBOX5
## 39:    HIST1H2BH       H2BC9
## 40:       FAM49A       CYRIA
## 41:        TTC37       SKIC3
## 42:      C1orf85        GLMP
## 43:     C9orf114      SPOUT1
## 44:   HIST2H2AA4      H2AC19
## 45:    HIST2H2BF      H2BC18
## 46:    C10orf128     TMEM273
## 47:     TCTEX1D2     DYNLT2B
## 48:     C17orf89     NDUFAF8
## 49:        PHBP3      PHB1P3
## 50:      SEPT7P7   SEPTIN7P7
## 51:    LINC00493      SMIM26
## 52:    HIST1H2BN      H2BC15
## 53:       ATP5J2      ATP5MF
## 54:        AKAP2  PALM2AKAP2
## 55:        WDR65      CFAP57
## 56:    SRP14-AS1    SRP14-DT
## 57: CTC-436P18.1  SMIM15-AS1
## 58:     HIST1H3G        H3C8
## 59:     EFTUD1P1      EFL1P1
## 60:     ATP5A1P3   ATP5F1AP3
## 61:     CCDC109B        MCUB
## 62:      C1orf63       RSRP1
## 63:       TMEM66       SARAF
## 64:       PCNXL2       PCNX2
## 65:         ACRC        GCNA
## 66:       AMICA1        JAML
## 67:       PRMT10       PRMT9
## 68:      FAM102A       EEIG1
## 69:         SELM     SELENOM
## 70:       NBPF16      NBPF15
## 71:       RPL9P9      RPL9P8
##      sym_in_data   sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma), gene_symbol := sym_limma]

dim(gene_info)
## [1] 1259    3
gene_info[1:5,]
##    sym_in_data sym_limma gene_symbol
## 1:    C1orf112  C1orf112    C1orf112
## 2:      MAD1L1    MAD1L1      MAD1L1
## 3:        ICA1      ICA1        ICA1
## 4:     NDUFAF7   NDUFAF7     NDUFAF7
## 5:         ST7       ST7         ST7
t1 = table(gene_info$gene_symbol)
table(t1)
## t1
##    1    2 
## 1255    2
gene_info[gene_symbol %in% names(t1)[t1 == 2],]
##    sym_in_data sym_limma gene_symbol
## 1:   HIST1H2BD     H2BC5       H2BC5
## 2:   HIST1H2BC     H2BC5       H2BC5
## 3:      RPL9P8    RPL9P8      RPL9P8
## 4:      RPL9P9    RPL9P8      RPL9P8
gene_info[sym_in_data == "HIST1H2BC", gene_symbol:="H2BC4"]
gene_info[sym_in_data == "RPL9P9", gene_symbol:="RPL9P9"]

Prepare gene set information

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]]    = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
gmtfile[["immune"]]   = "../Annotation/c7.all.v2023.2.Hs.symbols.gmt"

pathways = list()
for(k1 in names(gmtfile)){
  pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}

names(pathways)
## [1] "reactome" "go_bp"    "immune"
sapply(pathways, length)
## reactome    go_bp   immune 
##     1692     7647     5219

Filter gene sets for size between 10 and 500.

lapply(pathways, function(v){
  quantile(sapply(v, length), probs = seq(0, 1, 0.1), na.rm = TRUE)
})
## $reactome
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    7.0    9.0   12.0   17.0   23.0   31.0   44.0   71.8  120.9 1463.0 
## 
## $go_bp
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    6.0    8.0   10.0   14.0   19.0   29.0   46.0   80.8  183.0 1966.0 
## 
## $immune
##   0%  10%  20%  30%  40%  50%  60%  70%  80%  90% 100% 
##    5  162  193  197  199  199  200  200  200  200 1992
for(k1 in names(pathways)){
  p1 = pathways[[k1]]
  pathways[[k1]] = p1[sapply(p1, length) %in% 10:500]
}

Conduct enrichment analysis

dim(gene_info)
## [1] 1259    3
gene_info[1:2,]
##    sym_in_data sym_limma gene_symbol
## 1:    C1orf112  C1orf112    C1orf112
## 2:      MAD1L1    MAD1L1      MAD1L1
max_n2kp = 10

goseq_res = NULL

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info$sym_in_data %in% gene_sets[[k]]
  names(genes) = gene_info$gene_symbol
  table(genes)
  
  pwf = nullp(genes, "hg38", "geneSymbol")
  
  for(k1 in names(pathways)){
    p1 = pathways[[k1]]
    res1 = goseq(pwf, "hg38", "geneSymbol", 
                 gene2cat=goseq:::reversemapping(p1))
    res1$FDR  = p.adjust(res1$over_represented_pvalue, method="BH")
    
    nD = sum(res1$FDR < 0.05)
    
    if(nD > 0){
      res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
      res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
      res1$category = gsub("_", " ", res1$category)
      res1$category = tolower(res1$category)
      res1$category = substr(res1$category, start=1, stop=120)
      goseq_res[[set_k]][[k1]] = res1
    }
  }
}
## [1] 1
##  [1] "MCEE"          "RPS17"         "RPL34"         "RPS12"        
##  [5] "RPS25"         "RPL21"         "RPL5"          "RPS10"        
##  [9] "SGSM2"         "RPS27A"        "RPL32"         "RPS3A"        
## [13] "RPL7"          "RPL30"         "RPL9"          "RPS14"        
## [17] "RPL27A"        "RPLP2"         "RPS27"         "RPS23"        
## [21] "RPS26"         "RPL41"         "RPS18"         "CTD-2031P19.4"

## [1] 2
##  [1] "C1orf112"      "TNFRSF9"       "WDR13"         "ID3"          
##  [5] "CCRL2"         "YIPF2"         "FIGNL1"        "SLC2A8"       
##  [9] "SPPL2A"        "IRF8"          "CCDC51"        "SLC39A13"     
## [13] "KIR3DL1"       "GTSF1"         "ZBED2"         "YIPF6"        
## [17] "TNFRSF18"      "KIR2DL4"       "GM2A"          "KIR2DS4"      
## [21] "UBE2D3P2"      "RP4-742C19.12" "DBNDD2"        "RP11-511H9.4" 
## [25] "PHLDB3"        "ANKRD37"

## [1] 3
##  [1] "LTBP4"        "ARHGEF18"     "GPN2"         "FARP1"        "PPP1R32"     
##  [6] "C7orf55"      "TAF10"        "KBTBD2"       "ATPAF2"       "SGMS1"       
## [11] "RUFY2"        "PCNXL2"       "FAM117B"      "FBXO32"       "EPB41"       
## [16] "ATXN7"        "ZNF589"       "POLR2J3"      "YPEL2"        "NELL2"       
## [21] "TSC22D2"      "GPRASP1"      "PPP1R10"      "RP11-514P8.6" "HCG4P5"

## [1] 4
##  [1] "RNF10"     "CNOT2"     "C3orf14"   "AHI1"      "APTX"      "LINS"     
##  [7] "PLIN2"     "C2orf44"   "GLB1"      "RRM2"      "PCGF5"     "CNOT10"   
## [13] "EIF4ENIF1" "IFRD1"     "DDX3Y"     "TNRC6C"    "TNRC6B"    "UAP1"     
## [19] "YPEL5"     "CNOT6L"    "NR4A2"     "BTG2"      "PFKFB3"    "PLK3"

## [1] 5
##  [1] "RABGAP1"  "ERGIC2"   "GOSR2"    "CPD"      "NCOA7"    "MYB"     
##  [7] "NARF"     "MAP3K6"   "LIMD1"    "VPS37A"   "AGPAT6"   "C1orf123"
## [13] "WDR41"    "ASB8"     "HIST1H4C" "RAB12"    "DKK3"     "PPP2R5C" 
## [19] "CLDND1"   "ARRDC2"   "LEF1"     "SSH2"     "C9orf72"  "NPAT"    
## [25] "RALGAPA1"

## [1] 6
##  [1] "ICA1"    "GCFC2"   "GLT8D1"  "MAN2B1"  "GBP1"    "SCPEP1"  "SLC41A2"
##  [8] "CLSTN3"  "MFSD6"   "SLAMF8"  "USF1"    "ALG8"    "MTHFD2L" "GNGT2"  
## [15] "ITGAM"   "NINJ2"   "METRNL"  "TMEM107" "PRF1"    "BTLA"    "NCR3"   
## [22] "TRGV3"   "TREX1"   "KIR3DL2" "KIR2DL3"

## [1] 7
##  [1] "ZNRD1"   "TIMM9"   "POP4"    "POLR2I"  "GNPTAB"  "FAHD2A"  "EPAS1"  
##  [8] "GALE"    "UXT"     "TMEM241" "TIMM10"  "FHOD1"   "UCK2"    "MPPE1"  
## [15] "GALK2"   "MED11"   "LZTFL1"  "POLR2H"  "IL15"    "CDCA7L"  "POP5"   
## [22] "TRIM68"  "PPARA"   "UCKL1"   "SELM"

## [1] 8
##  [1] "FAM50B"        "FCRL6"         "CEP57L1"       "CALM2P3"      
##  [5] "RP11-773D16.1" "CTD-2521M24.9" "C1orf63"       "ACRC"         
##  [9] "AMICA1"        "CDC42EP3"      "ZMAT1"         "FILIP1L"      
## [13] "RBKS"          "CHD2"          "LDOC1"         "PLGLB1"       
## [17] "RP11-91K8.4"   "CTD-2328D6.1"  "PSMD6-AS2"     "MTND4P12"     
## [21] "RP11-727F15.9" "QRSL1P3"       "RP11-320M16.1" "RP11-335G20.7"
## [25] "RP11-51J9.5"

## [1] 9
##  [1] "CDKL1"         "PIM2"          "TFDP2"         "TTLL4"        
##  [5] "CASP1"         "APH1B"         "PSEN2"         "TMEM134"      
##  [9] "ANKRD28"       "TRAV24"        "PSMA6P1"       "RP11-122G18.7"
## [13] "RP1-182O16.1"  "RNU2-63P"      "PHBP3"         "RAB1C"        
## [17] "AC002331.1"    "NDUFA9P1"      "RP11-305L7.3"  "LINC00426"    
## [21] "RPL37P23"      "RP11-402J6.3"  "SNORD3A"       "PLXND1"       
## [25] "APBA2"         "PLA2G4B"

## [1] 10
##  [1] "ZNF419"           "PUS7L"            "NAALADL1"         "RP11-23P13.6"    
##  [5] "ZNF93"            "WDR53"            "C2orf76"          "ZNF28"           
##  [9] "RPSAP54"          "AC098614.2"       "XXbac-B562F10.11" "RP11-2F9.3"      
## [13] "RP3-342P20.2"     "RP11-567G24.1"    "RP11-247I13.6"    "AC115617.2"      
## [17] "GAPDHP2"          "CTD-2301A4.3"     "RPL7AP31"         "CTB-4E7.1"       
## [21] "RP11-307P22.1"    "TRAV30"           "RP11-209D14.4"    "CTB-31O20.3"     
## [25] "RP11-686D22.10"   "CTB-52I2.4"       "TMEM9B-AS1"

## [1] 11
##  [1] "SMG6"          "MS4A6A"        "C2orf43"       "L3HYPDH"      
##  [5] "PGPEP1"        "NPL"           "IFI44L"        "IFI44"        
##  [9] "TMEM138"       "TRANK1"        "EDARADD"       "TRGV10"       
## [13] "TRGV5"         "TRBV4-2"       "TRAV8-2"       "TRGC2"        
## [17] "ST13P19"       "RPL19P21"      "TRGV2"         "AC092580.4"   
## [21] "RP3-395M20.8"  "RP11-33B1.1"   "CCL3L3"        "CTD-2022H16.3"
## [25] "RP11-345J4.6"  "ATP5A1P3"

## [1] 12
##  [1] "PLA2G15"       "TRPT1"         "CMAHP"         "ZNF816"       
##  [5] "RP11-383G10.3" "AC144530.1"    "PKMP1"         "RP11-32B5.1"  
##  [9] "RP11-271C24.3" "STARD4-AS1"    "MAK"           "MAN1C1"       
## [13] "ACVR2A"        "NBPF14"        "C1orf162"      "PLAC8"        
## [17] "LDLRAP1"       "NBPF10"        "TMEM150A"      "CD248"        
## [21] "TRABD2A"       "NBPF16"        "AC084018.1"    "CTD-3092A11.1"
## [25] "RP11-632K20.7" "WHAMMP2"

## [1] 13
##  [1] "CHI3L2"        "CD200"         "PDE6B"         "KHDC1"        
##  [5] "MFSD9"         "FUOM"          "TNFAIP8L2"     "EFCAB4A"      
##  [9] "ZNF678"        "CPT1B"         "TRBV9"         "TRAV29DV5"    
## [13] "RP11-64B16.2"  "RP13-383K5.4"  "TPI1P2"        "RP11-782C8.1" 
## [17] "BDH2P1"        "SNRPEP4"       "LINC00484"     "BHLHE40-AS1"  
## [21] "RP11-179A18.1" "AC005329.7"    "SRP14-AS1"     "RP11-81H14.2" 
## [25] "KB-1507C5.2"   "USP30-AS1"     "AP000462.1"

## [1] 14
##  [1] "MFAP3"    "FAR2"     "SH3BP2"   "PTPN4"    "MICALL1"  "CAPN15"  
##  [7] "CRTAM"    "CD86"     "MTFR1L"   "HRSP12"   "DPH6"     "FGFBP2"  
## [13] "KSR1"     "FADS1"    "RNF207"   "CTLA4"    "FRS2"     "LRRC28"  
## [19] "ZNF80"    "PAAF1"    "CADM1"    "HIST1H4J" "SCML1"    "EPHA4"   
## [25] "MPP7"

## [1] 15
##  [1] "CENPQ"        "DHRS12"       "RASSF4"       "PRR4"         "CENPO"       
##  [6] "ARHGEF1"      "PIK3IP1"      "RGCC"         "EGR1"         "PMEPA1"      
## [11] "FOSB"         "JUND"         "SLC38A2"      "FAM102A"      "JUNB"        
## [16] "GOLGA8A"      "TTC3"         "RGPD6"        "MIR4461"      "MTND2P28"    
## [21] "MTND1P23"     "ATP1B3-AS1"   "RP11-44N11.1" "SLC7A5P1"     "KCNQ1OT1"

## [1] 16
##  [1] "WIPI1"  "DERL2"  "IL4R"   "ABHD11" "PTP4A1" "RCOR3"  "IFIT2"  "TEP1"  
##  [9] "RSAD2"  "FADS2"  "BCAS3"  "MX1"    "AMFR"   "FBXO22" "GNG4"   "BOLA1" 
## [17] "IFIT1"  "AGER"   "DNASE1" "PVT1"   "NEK1"   "SIK1"   "DHRS3"  "SERHL2"

## [1] 17
##  [1] "MAD1L1"   "CDC27"    "CDKN3"    "SPTLC2"   "ERCC2"    "GTF2H3"  
##  [7] "SMC4"     "CACYBP"   "CDC20"    "STMN1"    "CCR2"     "CKS2"    
## [13] "NPHP4"    "CCNB1"    "CDK7"     "PWP1"     "PMAIP1"   "CEP78"   
## [19] "HIRIP3"   "CCNB2"    "MYO1E"    "ANAPC10"  "SESTD1"   "C17orf89"
## [25] "TMEM63A"

## [1] 18
##  [1] "PTPN18"        "NT5C2"         "GALK1"         "GORASP1"      
##  [5] "STK25"         "CD160"         "DHDDS"         "NPC2"         
##  [9] "STYXL1"        "KATNBL1"       "WARS"          "TATDN1"       
## [13] "MITD1"         "AMDHD2"        "CTSB"          "GEM"          
## [17] "C11orf82"      "MEI1"          "TBCA"          "SMIM19"       
## [21] "SPATA13"       "PSMG1"         "ARHGAP11B"     "ANAPC10P1"    
## [25] "RP11-638I2.10"

## [1] 19
##  [1] "DYRK4"         "EGR2"          "DTD2"          "PIGW"         
##  [5] "CCDC30"        "AC018804.7"    "LDHBP2"        "MYL5"         
##  [9] "AC012318.3"    "RP11-350G8.3"  "GK3P"          "SKP1P1"       
## [13] "AC093391.2"    "RPS27AP2"      "CTC-338M12.4"  "PTGES3P1"     
## [17] "AP000476.1"    "AC018462.3"    "EEF1A1P10"     "HNRNPA1P16"   
## [21] "MIR3661"       "RP11-282O18.6" "RIMKLB"        "RP1-187B23.1" 
## [25] "RP13-488H8.1"  "LINC00944"     "RP11-1000B6.3"

## [1] 20
##  [1] "TM7SF3"         "GMPR2"          "DUS4L"          "LOXL3"         
##  [5] "FANCL"          "RNF121"         "TBCD"           "GEMIN6"        
##  [9] "CETN3"          "NDUFAF6"        "PAQR4"          "XRCC6BP1"      
## [13] "RHEBL1"         "NT5DC1"         "LRTOMT"         "TRAV13-1"      
## [17] "NCKIPSD"        "RP4-694B14.5"   "RPF2P1"         "GAPDHP73"      
## [21] "RPL13P5"        "CTC-436P18.1"   "PAICSP4"        "RP11-386G11.10"
## [25] "PMF1-BGLAP"     "ACTBP9"

## [1] 21
##  [1] "TBPL1"      "NSMAF"      "PMM1"       "GZMB"       "DDX49"     
##  [6] "BRD8"       "HAVCR1"     "MT2A"       "NARG2"      "PDZD2"     
## [11] "GTF2A2"     "DRAM2"      "GSTM4"      "CAPN12"     "COA3"      
## [16] "CMC1"       "ZNF765"     "CCL3L1"     "TRAV14DV4"  "LINC00493" 
## [21] "AC104820.2" "RN7SL749P"  "TPM3P6"     "AC004069.2" "AL358333.1"

## [1] 22
##  [1] "OCEL1"         "FAM45A"        "NME6"          "ZNF613"       
##  [5] "LCORL"         "EIF2S3L"       "ABHD16B"       "RPSAP47"      
##  [9] "TMEM194B"      "METTL6"        "RP11-12M9.4"   "CD27-AS1"     
## [13] "UBXN2B"        "ACTBP8"        "AC009506.2"    "AC010878.3"   
## [17] "CCT8P1"        "PGAM4"         "RP4-800M22.1"  "SEPT7P7"      
## [21] "PA2G4P4"       "PA2G4P2"       "RP11-446E9.1"  "RP11-473N11.2"
## [25] "RP11-317N8.4"  "RP11-493L12.6" "RP11-265N6.3"

## [1] 23
##  [1] "FAH"            "RRNAD1"         "TMSB15B"        "KIAA1841"      
##  [5] "LRRC45"         "SNHG11"         "AC004840.9"     "NAP1L4P1"      
##  [9] "GEN1"           "ZNF257"         "TRAV16"         "RP1-102E24.1"  
## [13] "ATF4P3"         "AC090804.1"     "ZNF826P"        "FAM21FP"       
## [17] "RP11-394D2.1"   "RNF138P1"       "MIR146A"        "SLC2A3P4"      
## [21] "SF3A3P2"        "RP11-416A17.6"  "RP11-304L19.5"  "RP11-1094M14.7"
## [25] "CTD-2545M3.2"   "RP11-705C15.5"

## [1] 24
##  [1] "ZNF268"        "MDGA1"         "MTERF"         "CX3CR1"       
##  [5] "ADCK5"         "THAP2"         "ZNF683"        "SLC9A9"       
##  [9] "CATSPER2P1"    "TRAV19"        "TRAV35"        "KANSL1-AS1"   
## [13] "RPS19P1"       "RPL19P12"      "RP11-119F19.2" "HNRNPKP2"     
## [17] "BTF3P10"       "ADH5P4"        "AC007041.2"    "RPS19P3"      
## [21] "GAPDHP60"      "RP11-613F22.5" "MIR3615"       "LUZP6"        
## [25] "RP11-297D21.4" "AC006129.4"    "LINC00674"

## [1] 25
##  [1] "IL18RAP"       "TNFSF10"       "PTGER2"        "MTHFS"        
##  [5] "ASNSD1"        "XCL1"          "XCL2"          "C9orf89"      
##  [9] "ZBTB39"        "MT1E"          "ENTPD5"        "MT1X"         
## [13] "ZNF720"        "C10orf128"     "TRBV20-1"      "RSC1A1"       
## [17] "NPM1P34"       "RP11-262H14.3" "RP11-693N9.2"  "ETF1P2"       
## [21] "HSPA8P4"       "HNRNPA1P55"    "TRGV7"         "TRAV1-2"      
## [25] "EFTUD1P1"      "HMGB1P8"       "CTD-3214H19.4"

## [1] 26
##  [1] "TIPIN"         "DUSP12"        "DEPDC5"        "NSMCE4A"      
##  [5] "RAD51C"        "AKR1A1"        "TXNDC17"       "TROAP"        
##  [9] "MMS22L"        "SFR1"          "PRIMPOL"       "UBE2C"        
## [13] "SWI5"          "ZBTB8OS"       "TYMS"          "POLE"         
## [17] "HIST1H2BC"     "HIST2H2AA4"    "STK19"         "MDP1"         
## [21] "RP11-365H23.1" "PIN4P1"        "PPIL3"         "HIST1H3G"

## [1] 27
##  [1] "REXO1"         "RP3-324O17.4"  "ZNF684"        "SLC35A5"      
##  [5] "TMEM19"        "C19orf55"      "MTHFD2P7"      "PLA2G6"       
##  [9] "TRAV12-2"      "TRDV1"         "TRDC"          "PDCL3P5"      
## [13] "RP5-1053E7.3"  "UBA52P6"       "LYPLA1P3"      "ARPC3P1"      
## [17] "RP11-350G13.1" "TCP1P1"        "PRDX3P1"       "RP11-288E14.2"
## [21] "MAPKAPK5-AS1"  "FAM200B"       "RNU1-125P"     "RP11-382J24.2"
## [25] "AC006483.1"    "AC139149.1"    "RP4-739H11.4"

## [1] 28
##  [1] "MAP3K13"       "OAS1"          "ZNF85"         "IL10"         
##  [5] "TMEM155"       "TECPR1"        "RP11-247I13.3" "TSTD1"        
##  [9] "PTGES3P2"      "PATL2"         "PET100"        "GYG1P3"       
## [13] "CNOT7P1"       "CDC42P1"       "Z97634.3"      "ZEB1-AS1"     
## [17] "GAPDHP38"      "RBBP4P1"       "RP11-889L3.4"  "AP000620.1"   
## [21] "RBBP4P5"       "RP11-1012A1.7" "TPMTP1"        "AC024592.12"  
## [25] "TCEAL3"        "AP001468.1"

## [1] 29
##  [1] "CD84"     "PON2"     "KLRB1"    "CCL4"     "ACTR10"   "KLRC1"   
##  [7] "BORA"     "GCHFR"    "CXCL13"   "PANK4"    "FCRL3"    "MGAT4B"  
## [13] "LGALS9C"  "SLC38A9"  "WRB"      "HLA-DQA1" "CCL4L2"   "FAM49A"  
## [19] "SH2D1B"   "MSH5"     "CCL4L1"   "KLRC2"    "TCTEX1D2" "SAPCD1"  
## [25] "MS4A1"

## [1] 30
##  [1] "AGA"     "GBA2"    "RNF13"   "USP48"   "RABGGTA" "GABPB1"  "GSR"    
##  [8] "ILVBL"   "PPFIA1"  "PPCDC"   "PPOX"    "TAMM41"  "SEC24D"  "FCGR3B" 
## [15] "RNF25"   "COG5"    "ZNF232"  "NFU1"    "ETFDH"   "MZT2A"   "TDRD7"  
## [22] "FCGR3A"  "NR1D2"   "WHAMMP3"

## [1] 31
##  [1] "MBNL3"    "AAAS"     "SLC25A14" "LIN7B"    "C17orf75" "COQ3"    
##  [7] "PRMT7"    "FOPNL"    "TPGS2"    "COPS3"    "LPP"      "CXXC1"   
## [13] "NTAN1"    "CTDNEP1"  "DALRD3"   "ZNF511"   "C1orf85"  "TMSB4X"  
## [19] "ATP5J2"   "ABHD14A"  "MIR142"   "GGT7"     "OBSCN"    "MUC20"   
## [25] "MALAT1"

## [1] 32
##  [1] "STAU2"    "NOP16"    "YBX3"     "NTHL1"    "DOT1L"    "DHX58"   
##  [7] "SLC11A2"  "DKC1"     "IMP4"     "SCRN2"    "PELP1"    "UTP23"   
## [13] "OXSM"     "FAM122B"  "DBF4B"    "ZFP62"    "ZNF431"   "ZNF770"  
## [19] "C9orf114" "ZBTB48"   "POTEG"    "MIR29B1"  "RPS11P5"  "AKAP2"

## [1] 33
##  [1] "WDR7"          "EMG1"          "DEF8"          "SPON2"        
##  [5] "HIST2H2BF"     "RPS12P26"      "GOT2P3"        "RP4-728D4.2"  
##  [9] "CTB-33G10.1"   "RASGRF2"       "AOAH"          "FRMD4A"       
## [13] "CXCR5"         "AC018720.10"   "FAM169A"       "HLA-J"        
## [17] "RPS26P6"       "RPS3AP26"      "RP11-572P18.1" "RPL10P3"      
## [21] "RPL9P8"        "RPL3P4"        "RPS3AP6"       "HLA-W"        
## [25] "RPL9P9"        "RPL9P7"

## [1] 34
##  [1] "CCL3"    "POLD3"   "P2RX5"   "KIF4A"   "ENO3"    "NR2C1"   "METTL8" 
##  [8] "DNPEP"   "SLC12A4" "SAT1"    "SNX14"   "PRSS23"  "TOMM40L" "TMPRSS3"
## [15] "B2M"     "LAIR2"   "DNAJC18" "METTL18" "AFMID"   "CRYGS"   "RGPD5"  
## [22] "STK17B"  "TMEM66"  "EIF1"    "CD55"

## [1] 35
##  [1] "NHP2P1"        "MCM9"          "PECR"          "NUDT7"        
##  [5] "CCDC28B"       "IFI27"         "ZNF749"        "EEF1GP1"      
##  [9] "ZNF649"        "ZNF525"        "NPM1P32"       "NPM1P33"      
## [13] "AC009403.2"    "RP11-378G13.2" "NPM1P19"       "RP11-270C12.3"
## [17] "HNRNPA1P21"    "RP11-809F4.2"  "TSEN15P1"      "RN7SL56P"     
## [21] "RP11-552M11.4" "GMPSP1"        "RP11-844P9.3"  "HMGB1P24"     
## [25] "RPPH1"         "RP11-265N6.2"  "RP13-638C3.4"

## [1] 36
##  [1] "EVC"          "NFE2L1"       "UBXN8"        "ZNF544"       "RASGRP2"     
##  [6] "MGAT4A"       "TXK"          "TCF7"         "SLC38A1"      "BACH2"       
## [11] "HECA"         "NR4A3"        "CCR7"         "PLXDC1"       "TIPARP"      
## [16] "PRMT10"       "DNHD1"        "ZBTB20"       "TSHZ2"        "KLHL25"      
## [21] "DENND5A"      "SELL"         "AC021593.1"   "LTB"          "RP11-285F7.2"
## [26] "ZNF10"        "RP11-747H7.3"

## [1] 37
##  [1] "VPS41"    "POLA2"    "USP28"    "WDR3"     "PIK3C3"   "ULK2"    
##  [7] "KHSRP"    "DHPS"     "THOC5"    "SNX8"     "NUP85"    "UROD"    
## [13] "C19orf47" "WDR43"    "BAP1"     "NAA15"    "MARS"     "ATG13"   
## [19] "DUSP28"   "PIK3R4"   "CHAMP1"   "MBD5"     "IFRD2"    "NAA16"

## [1] 38
##  [1] "ORMDL2"        "TRAV21"        "NAP1L1P3"      "RP3-340B19.5" 
##  [5] "GS1-124K5.2"   "EEF1A1P14"     "RP11-254B13.4" "RPSAP4"       
##  [9] "MTRNR2L3"      "HSPA8P5"       "HNRNPA1P50"    "ANP32AP1"     
## [13] "AL161784.1"    "CPQ"           "FOXP1"         "RCAN3"        
## [17] "BTG1"          "TC2N"          "GPR183"        "SATB1"        
## [21] "POU6F1"        "ACTBP12"       "CHRM3-AS2"     "CTD-2017D11.1"
## [25] "RP1-313I6.12"  "RP11-434H6.7"

## [1] 39
##  [1] "NDUFAF7"  "ACADVL"   "MTIF2"    "MRPS33"   "NDUFAF5"  "CDK5RAP1"
##  [7] "EARS2"    "MTFMT"    "SARS2"    "GTPBP10"  "THG1L"    "ATPAF1"  
## [13] "C6orf203" "MTO1"     "MRRF"     "GLUD1"    "MALSU1"   "MRPL55"  
## [19] "NDUFS4"   "METTL17"  "MRPL48"   "ZNF782"   "MRPL23"   "MRPL33"  
## [25] "CCDC109B"

## [1] 40
##  [1] "BCL3"       "GTSE1"      "RGS1"       "CCDC77"     "SMUG1"     
##  [6] "IFI6"       "GLUL"       "BRIP1"      "IRF4"       "PHAX"      
## [11] "HOPX"       "CXCR6"      "PDDC1"      "EFCAB7"     "RNU2-2P"   
## [16] "MIR155HG"   "AC011747.4" "DGKA"       "SKIL"       "RASGEF1B"  
## [21] "NPIPB3"     "PER1"       "NPIPB4"     "KLRK1"      "NPIPB5"    
## [26] "MTATP6P1"

for(n1 in names(goseq_res)){
  k = as.numeric(gsub("set_", "", n1))
  print(n1)
  print(gene_sets[[k]])
  print(goseq_res[[n1]])

}
## [1] "set_1"
##  [1] "MCEE"          "RPS17"         "RPL34"         "RPS12"        
##  [5] "RPS25"         "RPL21"         "RPL5"          "RPS10"        
##  [9] "SGSM2"         "RPS27A"        "RPL32"         "RPS3A"        
## [13] "RPL7"          "RPL30"         "RPL9"          "RPS14"        
## [17] "RPL27A"        "RPLP2"         "RPS27"         "RPS23"        
## [21] "RPS26"         "RPL41"         "RPS18"         "CTD-2031P19.4"
## $reactome
##                                                                                                  category
## 21  activation of the mrna upon binding of the cap binding complex and eifs and subsequent binding to 43s
## 117                                                                       cellular response to starvation
## 255                                                                     eukaryotic translation elongation
## 256                                                                     eukaryotic translation initiation
## 387                                                                                   influenza infection
## 471                                                             metabolism of amino acids and derivatives
## 547                                                                           nonsense mediated decay nmd
## 691                                                           regulation of expression of slits and robos
## 734                                                     response of eif2ak4 gcn2 to amino acid deficiency
## 783                                                                                       rrna processing
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat FDR
## 21                        0                        1         11       15   0
## 117                       0                        1         21       33   0
## 255                       0                        1         21       31   0
## 256                       0                        1         21       30   0
## 387                       0                        1         21       37   0
## 471                       0                        1         21       42   0
## 547                       0                        1         21       31   0
## 691                       0                        1         21       31   0
## 734                       0                        1         21       30   0
## 783                       0                        1         21       40   0
## 
## $go_bp
##                                category over_represented_pvalue
## 515             cytoplasmic translation            0.000000e+00
## 3691 ribosomal small subunit biogenesis            1.519549e-07
## 3693                ribosome biogenesis            3.069868e-07
##      under_represented_pvalue numDEInCat numInCat          FDR
## 515                         1         21       33 0.0000000000
## 3691                        1          7       16 0.0003105198
## 3693                        1          9       35 0.0004182183
## 
## $immune
##                                                                  category
## 54                        gaucher pbmc yf vax stamaril unknown age 7dy dn
## 1944                                gse22886 naive bcell vs neutrophil up
## 1974                                        gse22886 naive tcell vs dc up
## 2104               gse2405 0h vs 24h a phagocytophilum stim neutrophil up
## 2109                gse2405 0h vs 9h a phagocytophilum stim neutrophil dn
## 3108                           gse34205 healthy vs flu inf infant pbmc up
## 4014 gse41978 id2 ko vs id2 ko and bim ko klrg1 low effector cd8 tcell dn
## 4016                     gse41978 klrg1 high vs low effector cd8 tcell dn
## 1725                  gse21670 untreated vs tgfb il6 treated cd4 tcell dn
## 1628                      gse2124 ctrl vs lymphotoxin beta treated mln up
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 54              0.000000e+00                        1         12       32
## 1944            0.000000e+00                        1         12       25
## 1974            0.000000e+00                        1         12       33
## 2104            0.000000e+00                        1         16       40
## 2109            0.000000e+00                        1         15       37
## 3108            0.000000e+00                        1         11       25
## 4014            0.000000e+00                        1         11       32
## 4016            0.000000e+00                        1         12       30
## 1725            5.565068e-12                        1          9       17
## 1628            3.572682e-11                        1          9       19
##              FDR
## 54   0.00000e+00
## 1944 0.00000e+00
## 1974 0.00000e+00
## 2104 0.00000e+00
## 2109 0.00000e+00
## 3108 0.00000e+00
## 4014 0.00000e+00
## 4016 0.00000e+00
## 1725 3.15292e-09
## 1628 1.82171e-08
## 
## [1] "set_4"
##  [1] "RNF10"     "CNOT2"     "C3orf14"   "AHI1"      "APTX"      "LINS"     
##  [7] "PLIN2"     "C2orf44"   "GLB1"      "RRM2"      "PCGF5"     "CNOT10"   
## [13] "EIF4ENIF1" "IFRD1"     "DDX3Y"     "TNRC6C"    "TNRC6B"    "UAP1"     
## [19] "YPEL5"     "CNOT6L"    "NR4A2"     "BTG2"      "PFKFB3"    "PLK3"     
## $reactome
##                                                                                                             category
## 952 tp53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain
## 954                                                                 tp53 regulates transcription of cell cycle genes
## 981                                                                               transcriptional regulation by tp53
## 172                                                                                            deadenylation of mrna
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 952            5.539692e-08                1.0000000          5        6
## 954            4.270671e-07                1.0000000          5        8
## 981            2.121919e-05                0.9999986          7       35
## 172            9.227516e-05                0.9999994          3        4
##              FDR
## 952 5.661566e-05
## 954 2.182313e-04
## 981 7.228670e-03
## 172 2.357630e-02
## 
## $go_bp
##                                                                      category
## 1917                          nuclear transcribed mrna poly a tail shortening
## 1913 nuclear transcribed mrna catabolic process deadenylation dependent decay
## 3702                                                      rna destabilization
## 2380                            positive regulation of mrna metabolic process
## 1912                               nuclear transcribed mrna catabolic process
## 3201                                     regulation of mrna catabolic process
## 3202                                     regulation of mrna metabolic process
## 2179                        positive regulation of cellular catabolic process
## 1372                                                   mrna catabolic process
## 3257            regulation of nuclear transcribed mrna poly a tail shortening
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1917            3.257384e-11                1.0000000          7        8
## 1913            5.964863e-10                1.0000000          7       10
## 3702            1.204871e-08                1.0000000          7       14
## 2380            4.382508e-08                1.0000000          7       16
## 1912            4.542493e-08                1.0000000          7       15
## 3201            8.928398e-08                1.0000000          7       17
## 3202            4.629271e-07                1.0000000          7       21
## 2179            1.890462e-06                0.9999999          8       33
## 1372            2.026659e-06                0.9999999          7       24
## 3257            2.845476e-06                1.0000000          4        5
##               FDR
## 1917 1.331293e-07
## 1913 1.218920e-06
## 3702 1.641435e-05
## 2380 3.713034e-05
## 1912 3.713034e-05
## 3201 6.081727e-05
## 3202 2.702833e-04
## 2179 9.203284e-04
## 1372 9.203284e-04
## 3257 1.162946e-03
## 
## [1] "set_9"
##  [1] "CDKL1"         "PIM2"          "TFDP2"         "TTLL4"        
##  [5] "CASP1"         "APH1B"         "PSEN2"         "TMEM134"      
##  [9] "ANKRD28"       "TRAV24"        "PSMA6P1"       "RP11-122G18.7"
## [13] "RP1-182O16.1"  "RNU2-63P"      "PHBP3"         "RAB1C"        
## [17] "AC002331.1"    "NDUFA9P1"      "RP11-305L7.3"  "LINC00426"    
## [21] "RPL37P23"      "RP11-402J6.3"  "SNORD3A"       "PLXND1"       
## [25] "APBA2"         "PLA2G4B"      
## $reactome
##                category over_represented_pvalue under_represented_pvalue
## 858 signaling by notch3            2.616135e-05                0.9999999
##     numDEInCat numInCat        FDR
## 858          3        5 0.02673689
## 
## [1] "set_15"
##  [1] "CENPQ"        "DHRS12"       "RASSF4"       "PRR4"         "CENPO"       
##  [6] "ARHGEF1"      "PIK3IP1"      "RGCC"         "EGR1"         "PMEPA1"      
## [11] "FOSB"         "JUND"         "SLC38A2"      "FAM102A"      "JUNB"        
## [16] "GOLGA8A"      "TTC3"         "RGPD6"        "MIR4461"      "MTND2P28"    
## [21] "MTND1P23"     "ATP1B3-AS1"   "RP11-44N11.1" "SLC7A5P1"     "KCNQ1OT1"    
## $reactome
##                                                      category
## 544                              ngf stimulated transcription
## 564 nuclear events kinase and transcription factor activation
## 862                                        signaling by ntrks
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 544            8.510968e-06                0.9999999          4        7
## 564            1.210001e-05                0.9999999          4        8
## 862            3.174730e-05                0.9999994          4       10
##             FDR
## 544 0.006183104
## 564 0.006183104
## 862 0.010815248
## 
## [1] "set_17"
##  [1] "MAD1L1"   "CDC27"    "CDKN3"    "SPTLC2"   "ERCC2"    "GTF2H3"  
##  [7] "SMC4"     "CACYBP"   "CDC20"    "STMN1"    "CCR2"     "CKS2"    
## [13] "NPHP4"    "CCNB1"    "CDK7"     "PWP1"     "PMAIP1"   "CEP78"   
## [19] "HIRIP3"   "CCNB2"    "MYO1E"    "ANAPC10"  "SESTD1"   "C17orf89"
## [25] "TMEM63A" 
## $reactome
##                                                                                                                     category
## 456                                                                                                                  m phase
## 50                                                                              apc c cdc20 mediated degradation of cyclin b
## 138                                                                                 condensation of prometaphase chromosomes
## 500                                                                                           mitotic metaphase and anaphase
## 501                                                                                                     mitotic prometaphase
## 390 inhibition of the proteolytic activity of apc c required for the onset of anaphase by mitotic spindle checkpoint compone
## 52                                                                         apc c mediated degradation of cell cycle proteins
## 283                                                                               formation of rna pol ii elongation complex
## 286                                                                                formation of the early elongation complex
## 370                                                                                             hiv transcription elongation
##     over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 456            7.030593e-06                0.9999995          8       43
## 50             1.690017e-05                0.9999998          4        7
## 138            2.101969e-05                1.0000000          3        3
## 500            2.392556e-05                0.9999988          6       24
## 501            3.095286e-05                0.9999983          6       25
## 390            8.254878e-05                0.9999995          3        4
## 52             9.599288e-05                0.9999973          4       10
## 283            2.026152e-04                0.9999975          3        5
## 286            2.026152e-04                0.9999975          3        5
## 370            2.026152e-04                0.9999975          3        5
##             FDR
## 456 0.006112982
## 50  0.006112982
## 138 0.006112982
## 500 0.006112982
## 501 0.006326766
## 390 0.012942095
## 52  0.012942095
## 283 0.012942095
## 286 0.012942095
## 370 0.012942095
## 
## $go_bp
##                                  category over_represented_pvalue
## 1318  mitotic cell cycle phase transition            6.079680e-07
## 1221                   meiotic cell cycle            8.499976e-06
## 2926 regulation of chromosome segregation            2.116535e-05
##      under_represented_pvalue numDEInCat numInCat         FDR
## 1318                1.0000000          9       42 0.002484765
## 1221                0.9999996          6       20 0.017369700
## 2926                0.9999993          5       14 0.028834257
## 
## $immune
##                                                     category
## 3590 gse39556 cd8a dc vs nk cell mouse 3h post polyic inj up
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 3590            2.650089e-06                0.9999999          7       28
##            FDR
## 3590 0.0135128
## 
## [1] "set_26"
##  [1] "TIPIN"         "DUSP12"        "DEPDC5"        "NSMCE4A"      
##  [5] "RAD51C"        "AKR1A1"        "TXNDC17"       "TROAP"        
##  [9] "MMS22L"        "SFR1"          "PRIMPOL"       "UBE2C"        
## [13] "SWI5"          "ZBTB8OS"       "TYMS"          "POLE"         
## [17] "HIST1H2BC"     "HIST2H2AA4"    "STK19"         "MDP1"         
## [21] "RP11-365H23.1" "PIN4P1"        "PPIL3"         "HIST1H3G"     
## $reactome
##                           category over_represented_pvalue
## 212 dna replication pre initiation            2.649729e-05
## 211                dna replication            5.670078e-05
## 468          meiotic recombination            1.045790e-04
##     under_represented_pvalue numDEInCat numInCat        FDR
## 212                0.9999991          5       19 0.02708024
## 211                0.9999976          5       22 0.02897410
## 468                0.9999969          4       13 0.03562659
## 
## [1] "set_36"
##  [1] "EVC"          "NFE2L1"       "UBXN8"        "ZNF544"       "RASGRP2"     
##  [6] "MGAT4A"       "TXK"          "TCF7"         "SLC38A1"      "BACH2"       
## [11] "HECA"         "NR4A3"        "CCR7"         "PLXDC1"       "TIPARP"      
## [16] "PRMT10"       "DNHD1"        "ZBTB20"       "TSHZ2"        "KLHL25"      
## [21] "DENND5A"      "SELL"         "AC021593.1"   "LTB"          "RP11-285F7.2"
## [26] "ZNF10"        "RP11-747H7.3"
## $immune
##                                                                      category
## 1268                  gse17974 ctrl vs act il4 and anti il12 24h cd4 tcell up
## 56                                        goldrath eff vs memory cd8 tcell dn
## 136                                 gse11057 eff mem vs cent mem cd4 tcell dn
## 2958                 gse32255 wt unstim vs jmjd2d knockdown 4h lps stim dc up
## 3608                                gse3982 bcell vs cent memory cd4 tcell dn
## 2462 gse27241 wt vs rorgt ko th17 polarized cd4 tcell treated with digoxin dn
## 4597                           gse7219 unstim vs lps and anti cd40 stim dc up
## 4599              gse7219 unstim vs lps and anti cd40 stim nik nfkb2 ko dc up
## 5060                         scherer pbmc apsv wetvax age 18 32yo 5 to 7dy dn
## 425                        gse13547 ctrl vs anti igm stim zfx ko bcell 12h dn
##      over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1268            3.933068e-06                0.9999998          6       20
## 56              4.934628e-06                0.9999998          6       23
## 136             7.856450e-06                0.9999997          6       20
## 2958            1.125513e-05                0.9999995          6       22
## 3608            1.420646e-05                0.9999995          5       15
## 2462            2.907447e-05                0.9999989          5       16
## 4597            3.278495e-05                0.9999980          6       28
## 4599            4.373084e-05                0.9999972          6       29
## 5060            4.633864e-05                0.9999969          6       31
## 425             4.748952e-05                0.9999978          5       19
##             FDR
## 1268 0.01258083
## 56   0.01258083
## 136  0.01335335
## 2958 0.01434748
## 3608 0.01448775
## 2462 0.02388150
## 4597 0.02388150
## 4599 0.02421491
## 5060 0.02421491
## 425  0.02421491
## 
## [1] "set_38"
##  [1] "ORMDL2"        "TRAV21"        "NAP1L1P3"      "RP3-340B19.5" 
##  [5] "GS1-124K5.2"   "EEF1A1P14"     "RP11-254B13.4" "RPSAP4"       
##  [9] "MTRNR2L3"      "HSPA8P5"       "HNRNPA1P50"    "ANP32AP1"     
## [13] "AL161784.1"    "CPQ"           "FOXP1"         "RCAN3"        
## [17] "BTG1"          "TC2N"          "GPR183"        "SATB1"        
## [21] "POU6F1"        "ACTBP12"       "CHRM3-AS2"     "CTD-2017D11.1"
## [25] "RP1-313I6.12"  "RP11-434H6.7" 
## $immune
##                                          category over_represented_pvalue
## 1580 gse20727 h2o2 vs ros inhibitor treated dc up            1.940795e-07
##      under_represented_pvalue numDEInCat numInCat          FDR
## 1580                        1          5       19 0.0009896112
## 
## [1] "set_39"
##  [1] "NDUFAF7"  "ACADVL"   "MTIF2"    "MRPS33"   "NDUFAF5"  "CDK5RAP1"
##  [7] "EARS2"    "MTFMT"    "SARS2"    "GTPBP10"  "THG1L"    "ATPAF1"  
## [13] "C6orf203" "MTO1"     "MRRF"     "GLUD1"    "MALSU1"   "MRPL55"  
## [19] "NDUFS4"   "METTL17"  "MRPL48"   "ZNF782"   "MRPL23"   "MRPL33"  
## [25] "CCDC109B"
## $reactome
##                      category over_represented_pvalue under_represented_pvalue
## 495 mitochondrial translation            0.000000e+00                        1
## 986               translation            1.281153e-07                        1
##     numDEInCat numInCat          FDR
## 495          8        9 0.000000e+00
## 986         10       46 6.546692e-05
## 
## $go_bp
##                                 category over_represented_pvalue
## 1301       mitochondrial gene expression            0.000000e+00
## 1311           mitochondrial translation            0.000000e+00
## 1307 mitochondrial rna metabolic process            3.346653e-07
## 3989              trna metabolic process            2.827013e-05
##      under_represented_pvalue numDEInCat numInCat          FDR
## 1301                1.0000000         12       16 0.0000000000
## 1311                1.0000000         10       13 0.0000000000
## 1307                1.0000000          5        7 0.0004559257
## 3989                0.9999984          6       23 0.0288850024
## 
## [1] "set_40"
##  [1] "BCL3"       "GTSE1"      "RGS1"       "CCDC77"     "SMUG1"     
##  [6] "IFI6"       "GLUL"       "BRIP1"      "IRF4"       "PHAX"      
## [11] "HOPX"       "CXCR6"      "PDDC1"      "EFCAB7"     "RNU2-2P"   
## [16] "MIR155HG"   "AC011747.4" "DGKA"       "SKIL"       "RASGEF1B"  
## [21] "NPIPB3"     "PER1"       "NPIPB4"     "KLRK1"      "NPIPB5"    
## [26] "MTATP6P1"  
## $immune
##                                       category over_represented_pvalue
## 1806 gse22103 unstim vs lps stim neutrophil up            2.107416e-06
##      under_represented_pvalue numDEInCat numInCat        FDR
## 1806                        1          5       12 0.01074572
saveRDS(goseq_res, sprintf("output/gene_set_enrichments_%s.RDS", 
                           file_tag))

Session information

gc()
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8958527 478.5   17165476 916.8         NA 17165476 916.8
## Vcells 19141219 146.1   57216267 436.6      65536 78485130 598.8
sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.16.0
##  [2] GenomicFeatures_1.50.4                  
##  [3] GenomicRanges_1.50.2                    
##  [4] GenomeInfoDb_1.34.9                     
##  [5] org.Hs.eg.db_3.16.0                     
##  [6] AnnotationDbi_1.60.2                    
##  [7] IRanges_2.32.0                          
##  [8] S4Vectors_0.36.2                        
##  [9] Biobase_2.58.0                          
## [10] BiocGenerics_0.44.0                     
## [11] goseq_1.50.0                            
## [12] geneLenDataBase_1.34.0                  
## [13] BiasedUrn_2.0.10                        
## [14] fgsea_1.24.0                            
## [15] biomaRt_2.54.1                          
## [16] limma_3.54.2                            
## [17] tidyr_1.3.0                             
## [18] ggpubr_0.6.0                            
## [19] ggplot2_3.4.2                           
## [20] data.table_1.14.8                       
## 
## loaded via a namespace (and not attached):
##  [1] nlme_3.1-162                matrixStats_1.0.0          
##  [3] bitops_1.0-7                bit64_4.0.5                
##  [5] filelock_1.0.2              progress_1.2.2             
##  [7] httr_1.4.6                  tools_4.2.3                
##  [9] backports_1.4.1             bslib_0.4.2                
## [11] utf8_1.2.3                  R6_2.5.1                   
## [13] mgcv_1.8-42                 DBI_1.1.3                  
## [15] colorspace_2.1-0            withr_2.5.0                
## [17] tidyselect_1.2.0            prettyunits_1.1.1          
## [19] bit_4.0.5                   curl_5.0.1                 
## [21] compiler_4.2.3              cli_3.6.1                  
## [23] xml2_1.3.4                  DelayedArray_0.24.0        
## [25] rtracklayer_1.58.0          sass_0.4.5                 
## [27] scales_1.2.1                rappdirs_0.3.3             
## [29] Rsamtools_2.14.0            stringr_1.5.0              
## [31] digest_0.6.31               rmarkdown_2.21             
## [33] XVector_0.38.0              pkgconfig_2.0.3            
## [35] htmltools_0.5.5             MatrixGenerics_1.10.0      
## [37] dbplyr_2.3.2                fastmap_1.1.1              
## [39] rlang_1.1.0                 rstudioapi_0.14            
## [41] RSQLite_2.3.1               BiocIO_1.8.0               
## [43] jquerylib_0.1.4             generics_0.1.3             
## [45] jsonlite_1.8.4              BiocParallel_1.32.6        
## [47] dplyr_1.1.2                 car_3.1-2                  
## [49] RCurl_1.98-1.12             magrittr_2.0.3             
## [51] GO.db_3.16.0                GenomeInfoDbData_1.2.9     
## [53] Matrix_1.6-4                Rcpp_1.0.10                
## [55] munsell_0.5.0               fansi_1.0.4                
## [57] abind_1.4-5                 lifecycle_1.0.3            
## [59] stringi_1.7.12              yaml_2.3.7                 
## [61] carData_3.0-5               SummarizedExperiment_1.28.0
## [63] zlibbioc_1.44.0             BiocFileCache_2.6.1        
## [65] grid_4.2.3                  blob_1.2.4                 
## [67] parallel_4.2.3              crayon_1.5.2               
## [69] lattice_0.20-45             splines_4.2.3              
## [71] Biostrings_2.66.0           cowplot_1.1.1              
## [73] hms_1.1.3                   KEGGREST_1.38.0            
## [75] knitr_1.44                  pillar_1.9.0               
## [77] rjson_0.2.21                ggsignif_0.6.4             
## [79] codetools_0.2-19            fastmatch_1.1-3            
## [81] XML_3.99-0.14               glue_1.6.2                 
## [83] evaluate_0.20               png_0.1-8                  
## [85] vctrs_0.6.2                 gtable_0.3.3               
## [87] purrr_1.0.1                 cachem_1.0.7               
## [89] xfun_0.39                   broom_1.0.4                
## [91] restfulr_0.0.15             rstatix_0.7.2              
## [93] tibble_3.2.1                GenomicAlignments_1.34.1   
## [95] memoise_2.0.1